segment.{h,cpp}: align_against_collections with or without banded DP

This can be useful to align against a collection without the bandwidth
optimisation (see #2767).

algo/core/segment.cpp

@@ -836,12 +836,13 @@ bool comp_pair (pair<int,int> i,pair<int,int> j)
  * @param local:        if true, Local alignment (D segment), otherwise LocalEndWithSomeDeletions and onlyBottomTriangle (V and J segments)
  * @param box:          the AligBox to fill
  * @param segment_cost: the cost used by the dynamic programing
+ * @param banded_dp: should we perform a banded DP?
  * @post  box is filled
  */
 
 void align_against_collection(string &read, BioReader &rep, int forbidden_rep_id,
                               bool reverse_ref, bool reverse_both, bool local,
-                             AlignBox *box, Cost segment_cost)
+                              AlignBox *box, Cost segment_cost, bool banded_dp)
 {
   
   int best_score = MINUS_INF ;
@@ -858,6 +859,7 @@ void align_against_collection(string &read, BioReader &rep, int forbidden_rep_id
 
   // With reverse_ref, the read is reversed to prevent calling revcomp on each reference sequence
   string sequence_or_rc = revcomp(read, reverse_ref);
+  bool onlyBottomTriangle = !local && banded_dp ;
   
   for (int r = 0 ; r < rep.size() ; r++)
     {
@@ -870,7 +872,6 @@ void align_against_collection(string &read, BioReader &rep, int forbidden_rep_id
 			   reverse_both, reverse_both,
                           rep.read(r).marked_pos);
 
-      bool onlyBottomTriangle = !local ;
       int score = dp.compute(onlyBottomTriangle, BOTTOM_TRIANGLE_SHIFT);
       
       if (local==true){ 

algo/core/segment.h

@@ -390,6 +390,6 @@ class FineSegmenter : public Segmenter
 
 void align_against_collection(string &read, BioReader &rep, int forbidden_rep_id,
                               bool reverse_ref, bool reverse_both, bool local,
-                              AlignBox *box, Cost segment_cost);
+                              AlignBox *box, Cost segment_cost, bool banded_dp=true);
 
 #endif